on my network vlan1 is to be non routed management traffic between switches etc. vlan2 is general network vlan3 is wifi vlan4 is a point to point between routed interfaces vlan5 for servers.
Currently I have a trunk on port 3 of the isr so it can pass vlan1 & 3. I had just recently realized the reason my routed traffic was not going any where on the 6500 was due to my not using a layer3 interface (I think).
I have tried setting up port 2 on the isr as an access port with vlan4 as the native. I tried setting the layer3 on the 6500 as vlan4 and no response. I then tried sub-interfaces to get it to respond with no luck. it wont let me set vlan1 on sub-interfaces either so I suspect that wont work well either.
the isr has no issues routing to the internet. If I add a vlan2 address and set the isr as the gateway there are no issues getting out.